LAMMPS (28 Mar 2023 - Development)
  using 1 OpenMP thread(s) per MPI task
# 2d rounded polygon bodies

variable    r     index 4
variable    steps index 100000
variable    T     index 0.5
variable    P     index 0.1
variable    seed  index 980411

units       lj
dimension   2

atom_style  body rounded/polygon 1 6
atom_modify map array
read_data   data.squares
Reading data file ...
  orthogonal box = (0 0 -0.5) to (12 12 0.5)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  2 atoms
  2 bodies
  read_data CPU = 0.001 seconds

replicate   $r $r 1
replicate   4 $r 1
replicate   4 4 1
Replication is creating a 4x4x1 = 16 times larger system...
  orthogonal box = (0 0 -0.5) to (48 48 0.5)
  1 by 1 by 1 MPI processor grid
  32 atoms
  replicate CPU = 0.001 seconds

velocity    all create $T ${seed} dist gaussian mom yes rot yes
velocity    all create 0.5 ${seed} dist gaussian mom yes rot yes
velocity    all create 0.5 980411 dist gaussian mom yes rot yes

change_box  all boundary p f p
Changing box ...

variable cut_inner  equal 0.5
variable k_n        equal 100
variable k_na       equal 2
variable c_n        equal 0.1
variable c_t        equal 0.1
variable mu         equal 0.1
variable delta_ua   equal 0.5

pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 0.1 ${c_t} ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 0.1 0.1 ${mu} ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 0.1 0.1 0.1 ${delta_ua} ${cut_inner}
pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 ${cut_inner}
pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 0.5
pair_coeff * * ${k_n} ${k_na}
pair_coeff * * 100 ${k_na}
pair_coeff * * 100 2

comm_modify vel yes

neighbor     0.5 bin
neigh_modify every 1 delay 0 check yes

timestep     0.001

#fix         1 all nve/body
#fix         1 all nvt/body temp $T $T 1.0
fix          1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
fix          1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
fix          1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
fix          1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 fixedpoint 0 0 0

fix          2 all enforce2d
fix          3 all wall/body/polygon 2000 50 50 yplane 0.0 48.0

#compute      1 all body/local id 1 2 3
#dump         1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4]

thermo_style custom step ke pe etotal press
thermo       1000

#dump	     2 all image 10000 image.*.jpg type type zoom 2.0 #             adiam 1.5 body type 0 0
#dump_modify  2 pad 6

run          ${steps}
run          100000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 6.1568542
  ghost atom cutoff = 6.1568542
  binsize = 3.0784271, bins = 16 16 1
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair body/rounded/polygon, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/2d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.376 | 5.376 | 5.376 Mbytes
   Step         KinEng         PotEng         TotEng         Press     
         0   0.484375       0.25           0.734375       0.0067274306 
      1000   0.51464289     0.00099012638  0.51563301     0.013444625  
      2000   0.55653313     0.0040982283   0.56063136     0.0034505512 
      3000   0.75323998     0.023578898    0.77681887     0.0036652891 
      4000   0.70044978     0.092406287    0.79285607     0.0089262842 
      5000   0.54548803     0.096501313    0.64198934     0.0051379523 
      6000   0.48208829     0.097798861    0.57988715     0.015298049  
      7000   0.68219182     0.038843941    0.72103576     0.016842202  
      8000   0.53792445     0.012983807    0.55090825     0.0066797902 
      9000   0.49980359     0.029397948    0.52920154     0.0046731993 
     10000   0.48705779     0.10138799     0.58844578    -1.9696743e-05
     11000   0.52151792     0.065893508    0.58741142     0.0049365175 
     12000   0.59066419     0.039261015    0.62992521     0.001420608  
     13000   0.46059009     0.07386532     0.53445541     0.005654565  
     14000   0.37899234     0.13421331     0.51320565     0.0097199047 
     15000   0.49566894     0.052006844    0.54767578     0.00053157628
     16000   0.59294062     0.028393451    0.62133407     0.0057809461 
     17000   0.51260882     0.1266054      0.63921422     0.0021637817 
     18000   0.45603179     0.15710959     0.61314138     0.017707488  
     19000   0.52137969     0.1123825      0.63376219     0.015894031  
     20000   0.64553686     0.11579772     0.76133459     0.013239309  
     21000   0.38581837     0.17867419     0.56449256     0.0048572535 
     22000   0.42776514     0.12979071     0.55755585     0.008093469  
     23000   0.490055       0.14197765     0.63203265    -0.003575896  
     24000   0.57689881     0.10164831     0.67854712     0.022418321  
     25000   0.45630031     0.057905852    0.51420616     0.007959034  
     26000   0.59497685     0.193113       0.78808985     0.0076331679 
     27000   0.40943362     0.098595954    0.50802958     0.0016863757 
     28000   0.34512273     0.15696637     0.50208909     0.037435926  
     29000   0.59187862     0.1845377      0.77641632     0.014563665  
     30000   0.69204623     0.16392147     0.8559677      0.031708423  
     31000   0.40436029     0.34429435     0.74865464     0.073818847  
     32000   0.47580383     0.22708448     0.70288831     0.015795198  
     33000   0.48923447     0.23636413     0.72559861     0.025932606  
     34000   0.51960128     0.15145893     0.67106021    -0.00079607564
     35000   0.44792834     0.19927109     0.64719943    -0.0063461505 
     36000   0.54265821     0.17924788     0.72190609     0.017916439  
     37000   0.56020344     0.24977507     0.80997851     0.057844411  
     38000   0.28874871     0.21399353     0.50274224     0.022675277  
     39000   0.39030236     0.30170176     0.69200411     0.037482614  
     40000   0.4699469      0.20663643     0.67658333    -0.014082215  
     41000   0.50202447     0.21510708     0.71713155    -0.0063284222 
     42000   0.43029593     0.23511818     0.6654141      0.046478372  
     43000   0.41628842     0.21031596     0.62660438    -0.0053073644 
     44000   0.51101573     0.15862165     0.66963738     0.010251868  
     45000   0.56984114     0.18071709     0.75055823     0.021333409  
     46000   0.45510513     0.15385488     0.60896001     0.048441048  
     47000   0.41229547     0.20577222     0.61806769     0.027485704  
     48000   0.64114797     0.33672519     0.97787315     0.13522091   
     49000   0.44298056     0.27708867     0.72006923     0.026660315  
     50000   0.43250082     0.17778506     0.61028588     0.02714938   
     51000   0.59697891     0.25460003     0.85157894     0.026959715  
     52000   0.63110331     0.21528376     0.84638707     0.023157155  
     53000   0.46085491     0.25375607     0.71461099     0.024933391  
     54000   0.50772891     0.29280628     0.80053519     0.010621547  
     55000   0.67213557     0.2071375      0.87927307     0.061770903  
     56000   0.61184167     0.34686662     0.95870829     0.095262009  
     57000   0.42364554     0.29899934     0.72264488    -0.0080865129 
     58000   0.5033641      0.39810693     0.90147103     0.081474225  
     59000   0.61363438     0.25296035     0.86659472     0.041921315  
     60000   0.64600872     0.36997737     1.0159861      0.053833686  
     61000   0.43392277     0.29276613     0.7266889      0.054911225  
     62000   0.38910577     0.27714798     0.66625375    -0.0141031    
     63000   0.42343097     0.21637816     0.63980913    -1.6862315e-05
     64000   0.52512516     0.38797726     0.91310242     0.03170217   
     65000   0.48930994     0.4863269      0.97563684     0.025108671  
     66000   0.68354817     0.3629732      1.0465214      0.066714362  
     67000   0.5361863      0.44003399     0.97622029     0.1063525    
     68000   0.3605148      0.40138904     0.76190383     0.03287684   
     69000   0.62747502     0.49229352     1.1197685      0.053648724  
     70000   0.51326037     0.36561885     0.87887922     0.070871008  
     71000   0.45429341     0.38458357     0.83887698     0.010485881  
     72000   0.55377877     0.36434231     0.91812107     0.10507819   
     73000   0.6857324      0.45242968     1.1381621      0.022470322  
     74000   0.46349397     0.39082798     0.85432196     0.067650912  
     75000   0.59216869     0.32893138     0.92110008     0.0196582    
     76000   0.42985327     0.40674342     0.83659669     0.025700762  
     77000   0.54319568     0.55627833     1.099474       0.067233159  
     78000   0.59244798     0.5121155      1.1045635      0.12063624   
     79000   0.61140864     0.45505083     1.0664595      0.088578795  
     80000   0.64308346     0.4143502      1.0574337      0.038537249  
     81000   0.55053046     0.43357659     0.98410705     0.053930256  
     82000   0.54049882     0.41354335     0.95404217    -0.036458392  
     83000   0.47517728     0.30128468     0.77646196     0.0019488841 
     84000   0.57452781     0.1949493      0.76947711     0.039244382  
     85000   0.7907368      0.51406164     1.3047984      0.12766082   
     86000   0.59488507     0.50084726     1.0957323      0.080232158  
     87000   0.43071262     0.4682738      0.89898642     0.1266876    
     88000   0.53305256     0.55941308     1.0924656      0.17062068   
     89000   0.60672487     0.64951209     1.256237       0.17194524   
     90000   0.7134227      0.57323404     1.2866567      0.074617282  
     91000   0.65670871     0.58567381     1.2423825      0.025281565  
     92000   0.72364891     0.59755693     1.3212058      0.092201188  
     93000   0.69254418     0.75766186     1.450206       0.16036111   
     94000   0.56326058     0.6398442      1.2031048      0.26280736   
     95000   0.47480145     0.57734551     1.052147       0.039940021  
     96000   0.56909151     0.73081903     1.2999105      0.030223516  
     97000   0.53198039     0.71808155     1.2500619      0.033191485  
     98000   0.63572731     0.86931519     1.5050425      0.20901135   
     99000   0.64477038     0.76771721     1.4124876      0.059732095  
    100000   0.71275398     0.66613673     1.3788907      0.020038364  
Loop time of 2.21223 on 1 procs for 100000 steps with 32 atoms

Performance: 3905566.671 tau/day, 45203.318 timesteps/s, 1.447 Matom-step/s
96.4% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 1.1162     | 1.1162     | 1.1162     |   0.0 | 50.45
Neigh   | 0.0049629  | 0.0049629  | 0.0049629  |   0.0 |  0.22
Comm    | 0.045069   | 0.045069   | 0.045069   |   0.0 |  2.04
Output  | 0.00060169 | 0.00060169 | 0.00060169 |   0.0 |  0.03
Modify  | 1.0017     | 1.0017     | 1.0017     |   0.0 | 45.28
Other   |            | 0.04368    |            |       |  1.97

Nlocal:             32 ave          32 max          32 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:             19 ave          19 max          19 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:             59 ave          59 max          59 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 59
Ave neighs/atom = 1.84375
Neighbor list builds = 3214
Dangerous builds = 0
Total wall time: 0:00:02
